Kerbal Flight Indicators is a sort of alternative NavHud, I just pointed it out because it seems to have a different CameraClearFlags mode ("Nothing" instead of "Depth") but still has the transparency.

Adding to this, the transparency only shows up for me on surfaces that reflect sunlight. I didn't do elaborate tests with different light sources, it was more of a coincidence that I noticed this. Two screenshots from the same game. Other parts e.g. the stock fairings, have the same problem. https://imgur.com/a/0aJBfZS

Thank you!
With the camera "always on" in PWB Fuel Balancer it was more apparent than in NavHud so I started testing.
Took about three evenings of cycling through 200 mods. It was literally the last mod in my binary search because I put it in a group of "non-graphics related".
You can imagine how confused I was when I was done with the "graphics-related mods" and the issue was still there. I even looked through texture files trying to find something.
The transparency seems to require light (duh) on the surface, in my above screenshot the sun is in the west of KSC. So maybe it's a bug with the way the game does specular shaders? I have no idea how this works in Unity/KSP.
Edit: Two screenshots -- same game state. Against the light shows no transparency, but once you have a surface that reflects light you see it. https://imgur.com/a/0aJBfZS
A few further screenshots with other parts: https://imgur.com/a/w3liJBXB

Now that I'm closing in, I did some more testing and can also cause the same transparency when turning on Kerbal Flight Indicators or NavHud. So must be the camera they produce. Now if that's something unique to my system (nvidia) or a KSP issue... I've seen the transparency on Das's stream when he used NavHud.

I've seen similar transparency happen with Navhud. But I can produce the transparency just by installing the mod, it's not even activated in the above screenshot.
Maybe an issue with the InFlightMarkerCam?

I think I may have found an issue.
After a binary search through my mods, I'm almost certainly sure that this mod causes a transparency issue in my installation.
Log: https://mega.nz/#!Rwx0wCLa!8yE2AxQL-TYD6NOPgdVdlUXpblTyfhzoPEJbLphNxG0
Screenshot:

Currently preparing a heavily modded install of 1.6.1 (+KJR/Lisias), so far mostly CKAN. And it's not looking pretty... Sigh.
Log: https://mega.nz/#!gwASGQiS!U1gy5zRXOUYqC9MNIy8pNFuvo46AZmF5sWgL5Xtvuyo
It's completely shot, KJR has no chance of working. Don't even know where to start, so much is broken. Maybe a CKAN issue, too. Exceptions galore.
Log ends with a test vessel blowing up on launch xD
Edit: hm, why was B9_Aerospace_WingStuff in there to begin with. That's a mess. Seems to work now.

It persists, but I'll have to redo all my testing with the new model now. I get flickering of the cabin light when activating the RT antenna. https://remotetechnologiesgroup.github.io/RemoteTech/modders/modules/
I'll supply more info on what I tried but currently watching DasValdez.